World number one Nadal had only lost a set 6-0 at a grand slam on three previous occasions - the 2015 Australian Open, 2006 Wimbledon and the 2004 US Open - but that changed against rampant ninth seed Thiem in the opening set on Tuesday.
Nadal could easily have wrapped it up in the fourth set and missed five break points in the decider, but found a way to take one last opportunity against Thiem and his flowing single handed backhand.
The Spaniard had appeared the more tired of the two but he roused himself for one final effort and emerged victorious when Thiem sent a final smash long after four hours and 49 minutes.
Rafael Nadal had his longest match ever at the US Open on Tuesday, and he eventually emerged victorious over Dominic Thiem.
'It was a great battle and the conditions were tough, ' said the Spaniard of another sticky evening. Why? "I think because Basilashvili just relaxed, for the first two sets he is too far from the baseline, he is not doing too much with the ball", Wilander said.
"I don't think he's really sorry", said Thiem with a smile. "I played some good ones before, but not that long, not that long against the great guys on the Grand Slam stage", Thiem said.
AFTER almost five hours on court, world No.1 Rafael Nadal and rising challenger Dominic Thiem had exhausted their tanks.
The semi-final will pit Nadal against third seed Juan Martin del Potro for the second successive Grand Slam.
Thiem then grabbed a 4-3 lead in the third which he stretched to 5-3 but then it was his turn to crack as Nadal raced away with three games to claim a two sets to one lead.
That, Nadal would say afterward, managed to "break my heart. But in few days I will look back and will remember how great it was to play in front of a packed Arthur Ashe - this great match". I think we nearly all the time have great matches. But the last time, against Philipp Kohlschreiber in Miami last spring, he fought back to win the match. "I hope that we have many more in the future with a different end".
But while Isner was playing before what could count as a home crowd, del Potro got all manner of support throughout, from the blue-and-white flags or soccer jerseys dotting the stands to the repeated singsong chants of his nickname, "Delpo", punctuated by clapping.
Thiem was broken serving for the set and then could not hold on for the tie-break, saving two set points but not a third after planting a volley wide with the whole of the court available.
The Austrian was heartbroken but proud, saying: "It's going to be stuck in my mind forever".
The disappointment of failing to create a first match point seemed to weigh on him in the tiebreak and he played it dreadfully, showing rare confusion in going 0-3 down and then losing it 7-4. Del Potro, who has been the most dominant men's player this year, will have to go full throttle if he has to release Nadal's stranglehold over him.